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The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CYF PDB ENTRY 4CYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 THE PROTEIN WAS AT 15 MG/ML. THE RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE SET UP AT 8 C AND THE DROPS WERE 150 NL PLUS 150 NL IN SITTING DROP PLATES.
Crystal Properties Matthews coefficient Solvent content 3.91 68.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.904 α = 90 b = 101.904 β = 90 c = 133.652 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2013-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.89 47.6 99.7 0.21 14.5 16.3 18526
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3.04 97.9 1.12 2.7 16.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4CYF 2.89 88.25 17545 947 99.62 0.17646 0.17425 0.1786 0.21883 0.222 RANDOM 61.539
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 2.84 1.42 2.84 -9.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.198 r_dihedral_angle_4_deg 18.372 r_dihedral_angle_3_deg 15.288 r_dihedral_angle_1_deg 7.031 r_mcangle_it 4.309 r_scbond_it 3.816 r_mcbond_it 2.677 r_mcbond_other 2.675 r_angle_refined_deg 1.322 r_angle_other_deg 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.198 r_dihedral_angle_4_deg 18.372 r_dihedral_angle_3_deg 15.288 r_dihedral_angle_1_deg 7.031 r_mcangle_it 4.309 r_scbond_it 3.816 r_mcbond_it 2.677 r_mcbond_other 2.675 r_angle_refined_deg 1.322 r_angle_other_deg 0.71 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3615 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing